Throughout the series, the Intersect serves as the core of the storyline, as Bryce Larkin sent the First Intersect to Chuck. Various crime organizations strive to obtain the Intersect, or agents who have the Intersect in their head commonly referred as a human Intersect. Human Intersects will observe and analyze the encoded data they recently receive.

Following 9/11, the CIA and NSA were instructed to "play nice" and share their intelligence, in turn making it easier to track and identify threats to national security, and the manufactured Intersect is "how (they) did that." They put "every scrap of data (they) had" into the computer, and the Intersect "saw" patterns in the data that the agencies had not. For example, Chuck describes in "Chuck Versus the Intersect" that multiple agencies had picked up information suggesting a bombing attempt against General Stanfield during the speech he was due to give, but the CIA and NSA each only had part of the picture. The Intersect cross-checked and combined both groups' intelligence to determine the full nature of the threat. Dr. Howard Busgang (code name Perseus) was one of the technicians involved in its design and development, as was Dr. Jonas Zarnow. The chief designer is Stephen J. Bartowski (code name Orion), Chuck's father.

Stephen Bartowski was apparently unaware of what the government intended to do with the Intersect, and it is not entirely clear what he originally expected or if the government had designs for the Intersect beyond creating more powerful spies. Both he and Dr. Busgang refer ominously to Stephen learning about the government's plans for the Intersect. When Stephen did learn, after completing the original Cipher, he purged his personal records and went on the run.

In "Chuck Versus the Break-Up", Bryce leaves Chuck a pair of shades designed to update a human intersect, which at the time was Chuck. The shades needed the Intersect Data Drive in order perform the update to the Intersect with new intelligence.

In "Chuck Versus the Last Details", one of Chuck's flashes contains information on Vivian Volkoff's possible bases of operation - directly naming her in one of the encoded images. When Chuck last received an Intersect update, Vivian was not in command of Volkoff Industries, nor was she even aware of it's existence. This suggests that Chuck's Intersect is updated frequently with every new data from the CIA and NSA.